Robbing the Replicates
by Didiodo
Summary: Set in a Season 4 AU. Sheppard and his team manage to steal a space ship from the Replicators before its destroyed but find it holds more than Ancient Tech. Theses are the adventures of Sheppard as he fights the Replicators, Wraith and even Earth to keep Atlantis safe. Earth break away. Atlantis independence and formation of colony. John/OC. Possible Ancient return.


_**A/N: Hi, this is my second attempt at a story along this rough AU, my first wasn't so good. Some things will be slightly different in this fic compared to the series, that's mainly because I want it that way. **_

_**The will also be less of Teyla and Ronan, they'll still be there but at the moment I havn't planned them in a major characters.**_

_**This story will focus on John/OC relationship, the war with the Wraith and the building up of Atlantis from an expedition to a colony. **_

_**Enjoy =)**_

**Chapter 1**

"Look its simple." Rodney sighed looking around the table at the gathered Colonels, scientists, Wraith and Travellers who all showed there confusion.

"Just go over the plan once more for all us _Neanderthals_." Lieutenant Colonel John Sheppard said sarcastically to Rodney playing on his massive ego. Rodney sighed and prepared to say it all again.

"We've been trying to get rid of the Replicators by breaking the bonds that hold them together but they can build up immunity to this so we do the opposite." He paused for dramatic effect before continuing. "We increase the magnetic attraction between the nanites by so much that all of them will merge in to a massive sort of blob type thing."

"That does not solve our problem foolish human. You're just creating a super replicator that could be even more dangerous!" Todd, the Wraith, exclaimed making the security in the room raise their weapons at him. He settled down and the guns lowered.

"Well, when we do it there mass will be so great that it will sink into the planet causing an implosion that will destroy them for good. It will take time for them to adapt to their new form so they'll have almost no control… at least for a time anyway."

"And you're sure you can do this?" The Traveller representative questioned. Mckay couldn't hold back his smirk.

"Sure. All we got to is beam down a replicator of our own creation." Dr Mckay held up his hand to silence the protest of the room. "I would just be a bare model, it couldn't do much, no replicating, no violence. Perfectly safe." He paused to see if he had everyone convinced, no one voiced an objection so he assumed they were supportive.

"So where was I… Arhh, yes. We beam our own replicator that will be the centre of the attraction, and beam me and a security escort directly into their system core room where I'll make the necessary modifications and that's it. Replicators gone forever."

"How can you beam in there, surely they have shields to stop that." Colonel Carter said prompting the explanation she already knew.

"That the easy part, the Replicators, or the Ancients for that matter have never encountered beaming technology like ours so they won't know how to defend against it, but much like our anti-replicator weapons, if we allow them, they will find an effective way to block us so that is why we have to pull this off first time. We won't get a second chance like this… ever." Everyone around the long conference table nodded their agreement.

"If so, how do you plan to get out if they block our beaming _Doctor_?" An elderly General asked who looked like he liked this plan as much as he liked being on an alien planet; not very much.

"That's going to be tricky, yes, but I strongly believe that there will be a ship on the surface we can hijack and high tail it out of there." The General 'harrumphed'.

"Then I trust you'll be risking your own hide and not someone else's?" Rodney looked around the room for help but received none, if he denied than it would look like the plan was a suicide mission and would be called off but if he went than he could die! Mercifully John stepped in.

"I assure you General, Rodney will be going and me and my team will accompany him too. Now, What about the replicators in their ships?" John asked successful changing the topic away from the issues. Rodney sent him a thankful look.

"The fleet will have to hold them off long enough for them to be pulled in too. We're talking about and attraction at a proton level, if there any replicators in the system, they'll be pulled in. When they're all bonded the density of the blob will be astronomical. It will only take a few minutes for it to suck in all the Replicators and another few minutes for the planet to implode, which I might add, we won't want to be around for. As soon as it's done, we should all get to hyperspace."

"Have no fear doctor. The Hives will fight with you."

"You have the Travellers support too."

The Q&A went on for another hour with Rodney explaining the narrow window of opportunity they have while all the replicators are in one place and also how they have to keep the replicator fleet occupied until it's done. After the temporary alliance leaders had agreed upon a time and rendezvous point, they returned to their respective homes leaving Rodney and Colonel Sheppard in the conference room looking at the plan and Intel they were able to gather.

"It's a shame really." Rodney said wistfully. Sheppard arced an eyebrow at him questioningly. "Well they have all the technology the Ancients had, if not more and we're about to destroy it all."

"Well isn't there some way you can transfer their data before the planet explodes into itty bity pieces?"

"Nah, we don't have time. I'd have to get through all their encryptions which could take hours and then we have no fast way of transferring that amount of data before the planet becomes unstable."

"Don't fret Mckay, better no one has it than them having it. We shouldn't push our luck anyway, getting rid of the Replicators for good will be a miracle enough.

"Yeah, but just imagine what we could if we could salvage all the technology, the benefits to man kink would be immeasurable."

"But more importantly a whole lot of space ships to kick the Wraith right into the next dimension." Shepard smiled to himself imaging it, a whole fleet of Atlaintain Battleships. He heard Rodney slap his forehead in despair and soon they were both laughing.

"You're such a child, mention spaceships and you turn all giddy."

The two sat in silence for a while, just enjoying the peace and quiet. Soon they'd be off the to the rendezvous point and be an inch away from death… again as they take on the replicators in a do or die battle while they have to ally with the enemy to do so, it must be a Wednesday.

"Do you remember when all we had to worry about was the impending doom of a Wraith attack sucking our life from our bodies?" Shepard said quietly.

"They were good times, I'd almost give anything to go back there." They both sighed simultaneously.

John got up and moved towards the sliding doors before turning back to his best friend. "Get some rest, we got a long day ahead of us tomorrow."

* * *

"I still can believe Colonel Carter agreed to this." Rodney nervously mumbled as he paced on the bridge deck of the Deadalus going over his mission in his head over and over.

"It's a good plan, the benefits out-way the risks, that's why she agreed." Sheppard explained yet again trying to calm Rodney's nerves as everyone was reliant on him.

"I mean this is just suicide, what if they don't have a ship we can use, we'll be fried just like those metal munching bastards, that's what'll happen!"

"Rodney. Calm down. This was your plan, you'll do just fine."

"Ohh of course because my plans always work _so_ well." He replied with venom.

The gathered ships of Wraith, Travellers, Atlantis and Earth all jumped into hyperspace from the rendezvous point and started heading for the Replicator home world. People ran across the ship making final preparations, bolstering shield and weapons systems to be most effective, triple checking gear and giving motivational speeches.

Each commanding officer briefed their teams again as they prepared for combat on a scale they'd never fought on before. The fleet of mismatch space ships all emerged from hyperspace looking onto the Replicator home world and the many ships they had defending it.

"Fire all Batteries!" Colonel Caldwell ordered. All the ships engaged the Replicator fleet guarding the planet. "Beam down the Alpha squad." He barked and Mckay, John, Ronan, and a select group of five marines were consumed by a white light as they were beamed into the core control room, while Fran, the replicator Rodney had made the night before was beamed to another location.

As the group reappeared, a few quick shots from the marines cleared the room of replicators leaving small piles of ash in their wake. The room was large with a raised platform in the centre where 9 ZPMs where plugged in, and lots of thick cables extruding from it.

Rodney wasted no time walking up to it and plugging in his tablet, he tapped furiously as his lips mumbled something too quiet to hear.

John positioned his men at the only entrance with the anti replicator weapons at the ready, they would work for a while but the replicators would soon build up a resistance and they'd be as useless as bullets. Luckily it was quiet.

"Mckay! Hurry up, we're kinda on a clock here." Sheppard complained moving from foot to foot like an impatient child. Rodney spun to face the Colonel.

"I'm trying to single handily save this galaxy and maybe the universe so I think I deserve a bit of space and PEACE AND QUIET!"

"Alright, alright. Just hurry up. Their bound to be on their way."

"Sir, we got a situation. It's just been confirmed. They've blocked our signal. We can't be beamed out."

"Coms down too, Sir."

"We planned for this. Stay calm and everything will be fine." About a minute later the very stressed scientist announced it was done.

"Sorry Fran." He whispered so quietly, only Sheppard could hear it.

"Ok good job Rodney, Now let's high tail it to the nearest ship and be on our way." He tapped a few buttons and a holographic display appeared nearby. Ronan, John, Rodney were looking at the map to the Replicator home world, circled in red was an open area not too far from their current position with a ship inside.

"You want the good news or the bad news first?" Rodney asked having started typing again and swiping his hands across the display as boxes appeared and disappeared.

"There's bad news?" Ronan said drawing his sword tensing for danger.

"Just give it to us Doc." A soldier exclaimed. Replicators where, as they spoke, being sucked together which would soon enough make the planet unstable and they had no way out except that ship.

"Good news is the ships there and I currently reassigned every nearby replicator to prepare it for launch."

"Bad news?" Sheppard dared to ask.

"It won't be ready in time. It's built but not everything functional." Rodney mumbled hesitantly.

"Hyperdrive?" The Colonel gritted his teeth in suspense.

"Not exactly…"

"Going down in a blaze of fire than." Ronan grinned at the prospect of an honourable death while taking down his enemy.

"Not if I have anything to do with it, I enjoy life way too much. I'm uploading instructions to the ships main database to start patching in the software to jump start the ship and get us the hell out of here."

"Great." Sheppard said inflated with life again. "let's get a move we got minutes left."

"Can't. Still working my magic." The Colonel sighed, they didn't have time for delays.

"Ok, Ronan, take the men, get to the ship and secure it. Prep it for take off. I'll follow with Rodney as soon as humanly possible."

"Stay safe man." Ronan told his best friend as they grabbed each other's wrists in a sign of respect and did as ordered.

"Come on Rod, this is taking way too long, if you still want to be living, GET A MOVE ON!"

"We got plenty of time, besides I'm transferring the replicators main database into the ships. No point it all going to waste."

Before the Colonel could assault Rodney with every insulting word in his vocabulary, his com activated with Carter on the other side but with heavy inferences and white noise.

_"Sheppa... Repli..tors forming, get ... team out .. ..ere. Planet is abo.. to explode. .. .ou copy. ...epard! Do you r..d me. ..t out NOW! We can't ... much long..."_

_"I copy, we'll be fine. Get yourself to safety. Sheppard out."_

"Rodney! We have to leave now."

"Fine, Fine. But if you just give me a few more minutes ..." Sheppard grabbed Rodney and man handled him out the door.

They set out running as fast a Rodney was able, which was a lot slower than Sheppard would have liked. As they ran they could start to feel the effects of their plan more and more. The building started to crack and shake as the planets crust became unstable under the force of the Replicator blob.

They rounded a corner and they could see the transporter, one that could take them almost all the way to the ship that might or might not work. As they sped around the corner John quickly yanked Rodney back as 4 Replicators stood guard, there weapons fired and only just missed the humans.

John cocked his weapon and returned fire, using the corner as cover. The bullets from his MP40 simply slowed the machines down, but were almost ineffective. They continued to advance firing shot after shot of green, deadly energy.

"I hate to be a downer but we don't have time for this." Rodney told the Colonel in a hushed tone. Sheppard just laughed at the irony.

The Replicators rounded the corner and John managed to knock the guns out of two of their hands using the butt of his gun, but was backhanded into the wall with inhuman strength. The two Replicator who still held there weapons, raised them to John preparing to fire.

Rodney closed his eyes not being able to see his best friend die, when he opened them a few seconds later expecting to see his executioners, he only saw John struggling to rise from the floor.

"You just going to gork or are we going to get hell off this cursed planet."

"But .. bu..."

"They got sucked away, guess it working. Come on, before your geniuses kills us."

They stepped into the transporter, and a few clicks later, the doors opened to a large hanger, where a ship that was larger than an Arora class but built in a different style, was docked.

Before Rodney could spend there last moments commenting on the design of the ship, John forced Rodney into another run, with him panting heavily and John limping.

All around them was tools, or weapons and even some ZPMS that had been dropped by the replicators before they were whisked away into the metal stream that was moving across the sky.

The Colonel could see Mckays eyes wandering over the objects that a day ago would have been there top priory and now they were having to run past and leave to be destroyed.

The Sergeant of the Marine detachment was waiting for them, at the rear of the ship, clearly very tense as large cracks were starting to form beneath his feet.

"Thank God sir! The men have been hovering up all the supply's from nearby but we haven't had a chance to check the whole ship. Our readings say that the ships clean Sir."

"Excellent, where's the Bridge." Sheppard wasted no time.

"Straight ahead and to the left, Sir."

"Rodney keep up." and they were off again, racing through the ships corridors to the command centre of the ship where it could be piloted from. As John entered, lights turned on, panels powered up and displays appeared.

The two didn't need to discuss what to do, this wasn't the first Ancient ship they had to pilot that wasn't completely functional. John sat in the chair and it lit up under his mental command, the ships external doors started closing and the sub light engines started to raise them off the dying world just as the marines got aboard with arms piled high of ancient treasures.

Rodney started powering up the hyper drives, but they weren't fully functional yet. As much as he would have liked to bitch to Sheppard about how hard it would be get working, he just got on with it; his life was at stake after all.

As the ship rose over the world they could see from the sensors that the nearby space was clear of all friendly vessels but the debris of destroyed ships both friend and foe floated amongst the now empty fleet of battleships. The world started to crack and splinter as the fiery core was breached and spouts of fire erupted from the surface bathing the city magma. From their lofty altitude they could still see the silver blob of the replicators that spilled out of the city as it tried to gain some semblance of coordinated movement back but was being assaulted by the planet.

Soon after they were up, and too soon for Johns liking, the planet exploded sending rock, fire and other debris into the solar system just as Rodney managed to jump start the hyper drives into getting them out of there.

As they travelled through Hyperspace, safe for the first time in what seemed like weeks but was actually more like an hour, the new crew of the ship all gathered in the command centre and let out a sigh of relief, they'd done it.

Defeated the Replicators.

Just as the relieved laughs and jokes started surfacing amongst them, they felt the jolt as they dropped out of hyperspace; a lot sooner than the few hours it should have taken to get back to Atlantis. Outside, through the window to space, was no longer the multi-coloured spectrum of hyperspace but the black vacuum of space only disturbed by the solitary star with a small planet orbiting it, some distance away.

"Rodney..."

"Don't look at me. I told you the Hyperdrives weren't working."

"They were working a second ago." Ronan shouted threating Rodney, with narrowed eyes.

"Woh, easy chewie. Look like I told you it was a long shot anyway... I mean..."

"Hold up Doc, you didn't say anything like that." The Sergeant commented as his men nodded there agreement.

"I didn't? Ohh. Well basically the hyper drives don't work but I managed to trick them into getting us out of there. I just had no control over which direction or for how long we went. It's lucky we're still in the same Galaxy to be honest." Rodney had the good sense to seem embarrassed as he rubbed the back of his head.

"So what hell are we supposed to do now Mckay? We can't exactly sub light all the way to Atlantis can we?"

"Why don't you just do the same thing again?"

"No way! We try that again it'll rip this ship and us apart." The crew of 8 all looked in silence at Rodney than at Sheppard and back again for some magical solution to get them home again.

"There's no quick fix for this guys."

"Hey." A female marine shouted in protest.

"_Fine_, there's no quick fix, guys and gals, if we want to get out of here, we're going to need to finish installing all the ships software so we can fly her out of here alive and in one piece."

"OK, fine. How long will that take?" Colonel Sheppard asked, expecting an hour or may be 2 at the most.

"About a week." Rodney replied after a moment's thought. All of their jaws dropped.

"A Week! You've got to be kidding me." Ronan slumped into a nearby chair, he hated space as about as much as anyone can.

"Can't you... you know. Speed things along a bit." John asked deflated, even after the miraculous victory.

"Sorry. Not this time."

Sheppard turned to his men, he had to keep them busy and in good spirits. "You heard him. We got to spend a week here, so get over yourselves! Johnson, split your men into teams, we need supply's and a place to sleep. Ronan, see if there any jumpers anywhere and scout that planet for food and water. Rodney, get this ship working ASAP. Everyone stay on coms and alert."

There was a loud chorus of 'Yes Sir' from the military personal and a grumble from Rodney as they set about their assigned jobs.

Sheppard set out with Ronan heading back towards the rear of the ship to see what the Replicators, and his men were able to store aboard. The back was like a large warehouse that was wide and open with landing spaces for a lot of jumpers along the sides in two layer. Only 7 of those spaces held a jumpers which was still an amazing bonus but John could just picture having a fleet of about 50 jumpers at his disposal and felt a twinge of disappointment.

In the centre is lots of crates and boxes that could hold some useful equipment but what transported them into the ship was two, jumper like ships but were elongated with what appeared to be bigger engines and no weapons. They weren't secured during the take-off and had slid to the back crushing crates that seemed to hold some Replicator hand held weapons and some silvery looking rocks.

On the floor, where Replicators had probably been mid transport where scattered objects like smaller crates, parts of what appeared to be a panel of some sort, control crystals; some of which had been smashed, and of course what lit Johns face up the most was a few ZPMS that were more precious than gold.

_"Johnson, send a team to the hanger. We got lots of stuff to sort through_." He said over the coms by pressing the button on his ear piece.

_"There on the way Sir." _Replied the sergeant.

John gave Ronan a genuine smile, they had just gotten a huge lucky break, if they could get this all back to Atlantis, they could finally put the Wraith on the defensive.

The two friends talked for a while in good spirits about how they could blow up the Wraith in the best way, and even what they'd do after they'd won the war. Before they could get too excited, the inevitable happened, they got some bad news… well what seemed to be bad news at the time anyhow.

_"Erhh... Sir... I have a situation here. We've found... well I don't know how to explain it but you'd better get Dr Mckay here to check it out." _

_"Mckay's busy soldier. What do you need?"_

_"We're in section Delta Sir, you'd better see for yourself."_

Sheppard sighed, told Ronan to go ahead and help the team sort through all the stuff in the hanger before getting them to take him to scout the planet before leaving and heading towards section Delta.

As he arrived, he went into a medium sized room where two of his marines were looking quizzically at a tube like contraction with wires going in and out of its base. As Sheppard approached he couldn't understand what was so special about it but, as he got within a few metres he could see past the frosted glass to what had shocked them, there was a women in there.

An Ancient women.

_"Mckay. Get down here."_

_**A/N: Please Review and tell me what you thought and how I can improve.**_


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